Bacterial clearance and immune responses in a mouse model of pneumonia and a rat model of otitis media following parenteral or mucosal immunisation in both models were compared. Both the immunisation routes were equally effective in inducing bacterial clearance from the lung, upregulated the recruitment of white cells and lead to an increase in the concentration of TNF-α, IL-1β and specific antibody in the bronchoalveolar lavage. Both the routes of immunisation enhanced clearance of bacteria from the middle ear. Parenteral immunisation was most effective overall in enhancing bacterial clearance and recruiting white cells to the middle ear. Both the routes significantly suppressed the levels of TNF-α in the middle ear lavage. Mucosal immunisation induced a Streptococcus pneumoniae-specific IgA antibody response. Both the animal models gave highly reproducible disease and provided high levels of sensitivity for testing the efficacy of candidate vaccine antigens. Differences observed in the inflammatory responses require further study.